We use these models to predict the binding energies of transcription factor binding sites to within 1 kBT of their measured values. We further explore how such a sequence-energy mapping relates to the mechanisms of trancriptional regulation in various promoter contexts. Specifically, we show that ...
Transcription factors (TF) control gene expression by binding to their target DNA site to recruit, or block, the transcription machinery onto the promoter region of the gene of interest. Their function relies on the ability to find their target site quickly and selectively1. In living cells TFs...
Identification of transcription factor binding sites using ATAC-seq. Genome Biol. 20, 45 (2019). Article PubMed PubMed Central Google Scholar Baek, S., Goldstein, I. & Hager, G. L. Bivariate genomic footprinting detects changes in transcription factor activity. Cell Rep. 19, 1710–1722 (...
We retrieved 247 core-validated vertebrate transcript factor binding sites (TFBS) from theJASPAR 2024 database. Download thevertebrate dataset from here Download thebed files from hereas "jaspar_beds" Unpack and extract the relevant files from above. Place the contents intodata/TFBS/folder. ...
and most notablyDNA replicationwhich requires the joining of “Okazaki” fragments (the small, nascent ssDNA fragments generated from the copying of the minus strand). Initially searched forand found as a polynucleotide joining or sealing activity, DNA ligases are present ubiquitously in all living ...
During transcription, one strand of DNA serves as a template for synthesizing RNA (this DNA is known as the “minus,”“antisense,”“noncoding,”“anticoding” or “transcribed” strand). Transcription begins by RNA polymerase binding to a promoter sequence in DNA. In prokaryotes, accessory...
ALKBH1-binding inhibits H3K27me3 and promotes the expression of target genes.aIntegrative Genomics Viewer of 7 stress-related transcription factor genes targeted by ALKBH1.bThree regions (red horizontal bars) of the 7 genes tested by ChIP-PCR analysis with H3K27me3 and ALKBH1 antibodies.cRT-...
9c). This analysis further revealed that while gene length and DNA accessibility (based on ATAC-seq data) both correlated with transcription and CSB dependence, the strongest enriched feature of both gene sets was transcriptional activity (Fig. 7d and Extended Data Fig. 9d–f)....
Fig. 1: ES cells are viable in the absence of 5mC-binding MBD proteins and display limited changes in transcription and chromatin accessibility. a, Detection of MBD proteins by immunoblot in nuclear extracts from WT ES or two MBD–QKO clones (cl. 1 and 2) derived independently with differen...
Conversely, the successful DNA synthesis activity of HIV-1 RT at restrictive dNTP concentrations mechanistically results from its higher dNTP-binding affinity (75), which enables HIV-1 to complete viral reverse transcription in nondividing macrophages. Overall, these RTs may have evolved to display ...